Several reports at the Commons about non-existing pages that should exist. Examples at the time of writing:
Page should have been created at 2012-06-12, 00:01 UTC according to https://commons.wikimedia.org/w/index.php?title=Commons:Deletion_requests/2012/06/12&action=history
Probably the user used https://commons.wikimedia.org/wiki/MediaWiki:Gadget-AjaxQuickDelete.js to create this deletion nomination.
Then there's a whole series of uploaded files: https://commons.wikimedia.org/w/index.php?title=Commons:Administrators%27_noticeboard&oldid=72480417#Flickr2Commons_upload_bug
Presumably, Magnus's tool also uses the API to create pages. These files were uploaded around 2012-06-11 23:51 UTC.
In all cases, the page reports "The database did not find the text of a page that it should have found..."
Can this be related to the DB master switch around that time?